Have you tried moving around on the boat after jumping onto it?
Assuming you're not a Nosferatu, the guy you speak to should only shoot at you, if another guard spots you first. If that happens, he turns aggressive. If you are a Nosferatu, he'll get hostile once he sees you, regardless.
well once i got the sarcophagus viewed the report and manifest i was allowed to leave and the guy never shot at me even after i murdered every other cop.
The trigger on the Zodiac is the motor. Move toward it, and the boat will 'teleport' to the next destination.
Sic gorgiamos allos subjectatos nunc
(The Addams family motto: Gladly we feast on those who would subdue us)
Do not meddle in the affairs of Dragons, for you are crunchy, and good with Ketchup.